Projectes de modelatge i simulació avançada de sistemes mitjançant l'entorn ARENA

En l’exercici de les funcions típiques de qualsevol activitat humana, l’home ha de prendre decisions d’un o altre tipus permanentment i aquesta situació porta afegit, per lo general risc i incertesa, el que compromet la qualitat i l’èxit de la decisió. Per ajudar i contrarestar aquesta situació, l’home ha desenvolupat a través del temps una diversitat d’eines que li permeten minimitzar el risc i la incertesa en la presa de decisions. La simulació és una d’aquestes eines. Mitjançant la seva aplicació no només s’aconsegueix la comesa anterior, sinó que també es minimitzen els costos involucrats en la decisió mitjançant un millor ús dels recursos, la disminució del temps emprat per a la seva realització i la minimització de les probabilitats de risc. Aquest projecte representa la continuació d’un primer estudi introductori de la simulació anomenat: Estudi i guia docent per a modelatge i simulació de sistemes mitjançant l’entorn ARENA [9]. Realitzat per l’alumna d’Enginyeria en Organització Industrial de la Universitat de Vic, Montse Carbonell Crosas, l’any 2008 i sota la codirecció del director d’aquest segon projecte, el professor Juli Ordeix Rigo. Aquest nou projecte s’inicia amb una primera part teòrica, continguda dins del primer volum, la qual reforça els conceptes teòrics referents a la simulació amb ARENA, ja vistos en l’anterior projecte. Complementant aquells considerats bàsics i els de més utilitat i finalitza introduint nous conceptes avançats. Els nous capítols de temàtica avançada, junt als primers més bàsics de la primera part són exercitats dins de la segona, formant el segon volum d’aquest projecte. El mateix requereix la participació activa de l’alumne, per tal de realitzar cadascun dels 89 exercicis pràctics que es plantegen i poder onsolidar l’aprenentatge teòric d’aquesta eina avançada de simulació fent consultes als apartats teòrics recomanats dins de cada exercici. La complexitat dels exercicis anirà augmentant gradualment i s’insisteix en seguir la metodologia presentada en el projecte per a realitzar-los tots de forma ordenada i ascendent. L’ alumne quan acabi la part pràctica, haurà consolidat tota la part teòrica i serà capaç d’exercir com analista per tal de generar els seus propis projecte de simulació.

Dinámica del heleoplancton en relación a las fluctuaciones hidrológicas en aiguamolls de l’Empordà (NE de la península Ibérica). Propuesta de un método sencillo de monitorización basado en la abundancia de grupos taxonómicos

Monitoring of the 'ecological water quality' in 'Aiguamolls de l’Empordà' Natural Park was carried out between September 1996 and August 1997 . The aim of this sampling programme was to design a simple method for rapid detect changes in water quality due to human activity. These include flow regulation by the Park management, nutrient entries from effluents of a nearby wastewater treatment plant or agricultural fertilising. The proposed method is based on the analysis of the abundance of characteristic taxonomic groups of aquatic invertebrates (heleoplankton). The simplicity of the method is ensured by the use of large taxa which are easier to recognise than species. The functioning of aquatic systems has been modelled by means of correspondence analysis between samples and taxa. Results can be summerized in five environmental conditions with a regular community structure. Dominated by one taxon: cladocerans, ostracods, calanoids, cyclopoids and harpacticoids. The dynamics of both freshwater and brackish lagoons can be modelled as displacements between these five groups of environmental conditions. Nevertheless, the “calanoids situation” and the “harpacticoids situation” occur mainly in brackish lagoons, whereas the “cladocerans situation” occurs mainly in freshwater. The four principal axes of data variation have been respectively identified as nutrient turnover rate, hypertrophy, degree of mineralization of the organic matter and eutrophy. The use of these taxa has been validated by comparison with a model obtained from the species. We conclude that in a highly fluctuating system such as the one here, only persistent situations of eutrophy or hypertrophy must be equated to low 'ecological water quality'

Dance movement patterns recognition

"Es tracta d'un projecte dividit en dues parts independents però complementàries, realitzades per autors diferents. Aquest document conté originàriament altre material i/o programari només consultable a la Biblioteca de Ciència i Tecnologia"

Evaluation of free libraries for visual recognition of art imagery on mobile devices

This paper describes a systematic research about free software solutions and techniques for art imagery computer recognition problem.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: We present the results of EGASP, a community experiment to assess the state-ofthe-art in genome annotation within the ENCODE regions, which span 1% of the human genomesequence. The experiment had two major goals: the assessment of the accuracy of computationalmethods to predict protein coding genes; and the overall assessment of the completeness of thecurrent human genome annotations as represented in the ENCODE regions. For thecomputational prediction assessment, eighteen groups contributed gene predictions. Weevaluated these submissions against each other based on a ‘reference set’ of annotationsgenerated as part of the GENCODE project. These annotations were not available to theprediction groups prior to the submission deadline, so that their predictions were blind and anexternal advisory committee could perform a fair assessment.Results: The best methods had at least one gene transcript correctly predicted for close to 70%of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into accountalternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotidelevel, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programsrelying on mRNA and protein sequences were the most accurate in reproducing the manuallycurated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could beverified.Conclusions: This is the first such experiment in human DNA, and we have followed thestandards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe theresults presented here contribute to the value of ongoing large-scale annotation projects and shouldguide further experimental methods when being scaled up to the entire human genome sequence.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

Platform for Automatic, Normalized Annotation and Cost-Effective Acquisition of Language Resources for Human Language Technologies: PANACEA

El objetivo de PANACEA es engranar diferentes herramientas avanzadas para construir una fábrica de Recursos Lingüísticos (RL), una línea de producción que automatice los pasos implicados en la adquisición, producción, actualización y mantenimiento de los RL que la Traducción Automática y otras tecnologías lingüísticas, necesitan.

PANACEA (Platform for Automatic, Normalised Annotation and Cost-Effective Acquisition of Language Resources for Human Language Technologies)

The objective of PANACEA is to build a factory of LRs that automates the stages involved in the acquisition, production, updating and maintenance of LRs required by MT systems and by other applications based on language technologies, and simplifies eventual issues regarding intellectual property rights. This automation will cut down the cost, time and human effort significantly. These reductions of costs and time are the only way to guarantee the continuous supply of LRs that MT and other language technologies will be demanding in the multilingual Europe.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

Entamoeba lysyl-tRNA synthetase contains a cytokine-like fomain with chemokine activity towards human endothelial cells

Immunological pressure encountered by protozoan parasites drives the selection of strategies to modulate or avoid the immune responses of their hosts. Here we show that the parasite Entamoeba histolytica has evolved a chemokine that mimics the sequence, structure, and function of the human cytokine HsEMAPII (Homo sapiens endothelial monocyte activating polypeptide II). This Entamoeba EMAPII-like polypeptide (EELP) is translated as a domain attached to two different aminoacyl-tRNA synthetases (aaRS) that are overexpressed when parasites are exposed to inflammatory signals. EELP is dispensable for the tRNA aminoacylation activity of the enzymes that harbor it, and it is cleaved from them by Entamoeba proteases to generate a standalone cytokine. Isolated EELP acts as a chemoattractant for human cells, but its cell specificity is different from that of HsEMAPII. We show that cell specificity differences between HsEMAPII and EELP can be swapped by site directed mutagenesis of only two residues in the cytokines' signal sequence. Thus, Entamoeba has evolved a functional mimic of an aaRS-associated human cytokine with modified cell specificity.

The promoter activity of human Mfn2 depends on Sp1 in vascular smooth muscle cells

AIMS: Mitofusin-2 (Mfn2) expression is dysregulated in vascular proliferative disorders and its overexpression attenuates the proliferation of vascular smooth muscle cells (VSMCs) and neointimal lesion development after balloon angioplasty. We sought to gain insight into the mechanisms that control Mfn2 expression in VSMCs. METHODS AND RESULTS: We cloned and characterized 2 kb of the 5'-flanking region of the human Mfn2 gene. Its TATA-less promoter contains a CpG island. In keeping with this, 5'-rapid amplification of cDNA ends revealed six transcriptional start sites (TSSs), of which TSS2 and TSS5 were the most frequently used. The strong CpG island was found to be non-methylated under conditions characterized by large differences in Mfn2 gene expression. The proximal Mfn2 promoter contains six putative Sp1 motifs. Sp1 binds to the Mfn2 promoter and its overexpression activates the Mfn2 promoter in VSMCs. Chemical inhibition of Sp1 reduced Mfn2 expression, and Sp1 silencing reduced transcriptional activity of the Mfn2 promoter. In keeping with this view, Sp1 and Mfn2 mRNA levels were down-regulated in the aorta early after an atherogenic diet in apolipoprotein E-knockout mice or in VSMCs cultured in the presence of low serum. CONCLUSION: Sp1 is a key factor in maintaining basal Mfn2 transcription in VSMCs. Given the anti-proliferative actions of Mfn2, Sp1-induced Mfn2 transcription may represent a mechanism for prevention of VSMC proliferation and neointimal lesion and development.

The promoter activity of human Mfn2 depends on Sp1 in vascular smooth muscle cells

AIMS: Mitofusin-2 (Mfn2) expression is dysregulated in vascular proliferative disorders and its overexpression attenuates the proliferation of vascular smooth muscle cells (VSMCs) and neointimal lesion development after balloon angioplasty. We sought to gain insight into the mechanisms that control Mfn2 expression in VSMCs. METHODS AND RESULTS: We cloned and characterized 2 kb of the 5'-flanking region of the human Mfn2 gene. Its TATA-less promoter contains a CpG island. In keeping with this, 5'-rapid amplification of cDNA ends revealed six transcriptional start sites (TSSs), of which TSS2 and TSS5 were the most frequently used. The strong CpG island was found to be non-methylated under conditions characterized by large differences in Mfn2 gene expression. The proximal Mfn2 promoter contains six putative Sp1 motifs. Sp1 binds to the Mfn2 promoter and its overexpression activates the Mfn2 promoter in VSMCs. Chemical inhibition of Sp1 reduced Mfn2 expression, and Sp1 silencing reduced transcriptional activity of the Mfn2 promoter. In keeping with this view, Sp1 and Mfn2 mRNA levels were down-regulated in the aorta early after an atherogenic diet in apolipoprotein E-knockout mice or in VSMCs cultured in the presence of low serum. CONCLUSION: Sp1 is a key factor in maintaining basal Mfn2 transcription in VSMCs. Given the anti-proliferative actions of Mfn2, Sp1-induced Mfn2 transcription may represent a mechanism for prevention of VSMC proliferation and neointimal lesion and development.

Visual SLAM for underwater vehicles using video velocity log and natural landmarks

A visual SLAM system has been implemented and optimised for real-time deployment on an AUV equipped with calibrated stereo cameras. The system incorporates a novel approach to landmark description in which landmarks are local sub maps that consist of a cloud of 3D points and their associated SIFT/SURF descriptors. Landmarks are also sparsely distributed which simplifies and accelerates data association and map updates. In addition to landmark-based localisation the system utilises visual odometry to estimate the pose of the vehicle in 6 degrees of freedom by identifying temporal matches between consecutive local sub maps and computing the motion. Both the extended Kalman filter and unscented Kalman filter have been considered for filtering the observations. The output of the filter is also smoothed using the Rauch-Tung-Striebel (RTS) method to obtain a better alignment of the sequence of local sub maps and to deliver a large-scale 3D acquisition of the surveyed area. Synthetic experiments have been performed using a simulation environment in which ray tracing is used to generate synthetic images for the stereo system